On my Dell D400 laptop I got that message from kernel on boot:

[   26.256057] PCI: Transparent bridge - 0000:00:1e.0
[   26.256125] PCI: Bus #02 (-#05) is hidden behind transparent bridge #01 
(-#01) (try 'pci=assign-busses')
[   26.256132] Please report the result to linux-kernel to fix this 
permanently
[   26.256169] PCI: Bus #06 (-#09) is hidden behind transparent bridge #01 
(-#01) (try 'pci=assign-busses')
[   26.256175] Please report the result to linux-kernel to fix this 
permanently

I added "pci=assign-busses" into kernel cmdline and everything is working 
without problems. And I did not noticed problems without it.

Attached files:

lspci-vvv.text is output of "lspci -vvv"
dmesg-nopci.text is dmesg output without "pci=assign-busses"
dmesg-pci.text is dmesg output with "pci=assign-busses"